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This Week in PNAS: Feb 9, 2010

This week in the PNAS Early Edition, researchers show a relationship between RNA polymerases II and III by using ChIP-Seq studies to map their in vivo binding sites throughout the human genome. In the investigation of two cell lines, GM12878 and K562, Pol II was found to bind near many known Pol III genes, as well as a number of previously unidentified Pol III targets. The team also found that transcription factors normally associated with Pol II transcription were also closely connected with Pol-III-transcribed genes. Their results refute the previous expectation that RNA polymerases operate independently from one another, showing that Pol II and Pol III can work together to globally coordinate gene expression.

Research of out of Iowa State University demonstrates that AtIWS1, a protein implicated with the post-recruitment and transcription elongation processes of RNA polymerase II in Arabadopsis thaliana, is required for brassinosteroid-induced gene expression. The researchers found that loss-of-function mutations in AtIWS1 resulted in overall dwarfism, hypersensitivity to a transcription elongation inhibitor, reduced BR response, and, therefore, a genome-wide decrease in BR-induced expression in the model plant. The team writes that their study establishes an important role for AtIWS1 in plant steroid-induced gene expression and also suggests the possibility that the protein can be used as a target for pathway-specific activators in Arabidopsis.

In this week's advance online publication of PNAS, California Institute of Technology researchers discuss connections within the neural crest gene regulatory network, specifically the function of Sox10 as one of the earliest neural crest-specifying genes. The team found that Sox10 drives delamination and directly regulates several downstream effectors and differentiation gene batteries. In performing ChIP, DNA pull-down, and gel-shift assay experiments, the team also demonstrates Sox10E2 - the earliest acting neural crest cis-regulatory element-binding to its enhancer in vivo. This cis-regulatory analysis helped the researchers to establish the direct link of upstream effectors to a key neural crest specifier.

Also in PNAS this week, Markus Rinschen and his international colleagues describe their use of mass spectrometry-based quantitative phosphoproteomics to identify signaling pathways involved in the short-term V2-receptor-mediated response in murine renal collecting duct cells. Using the mouse model, Rinschen's team created two treatment groups: one received 0.1 nM dDAVP, the other merely the treatment vehicle. In the quantification of 2884 phosphopeptides, the researchers establish the roles of multiple V2-receptor-dependent signaling pathways in the vasopression signaling network of collecting duct cells.

The Scan

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.

Study Highlights Pitfall of Large Gene Panels in Clinical Genomic Analysis

An analysis in Genetics in Medicine finds that as gene panels get larger, there is an increased chance of uncovering benign candidate variants.

Single-Cell Atlas of Drosophila Embryogenesis

A new paper in Science presents a single-cell atlas of fruit fly embryonic development over time.

Phage Cocktail Holds Promise for IBD

Researchers uncovered a combination phage therapy that targets Klebsiella pneumonia strains among individuals experiencing inflammatory bowel disease flare ups, as they report in Cell.